library(GOplot)
Loading required package: ggplot2
Loading required package: ggdendro
Loading required package: gridExtra
Loading required package: RColorBrewer
name <- 'heatmap_logFC0.3_ncluster6'
folder <- paste('../tables/BEAM/', name, sep='')
gsea_files <- list.files(paste(folder, '/REVIGO_cleaned/', sep=''))
clusters <- c(1,2,3,4,6)
gsea <- list()
genelist <- list()
for (i in clusters){
gsea_cluster <- read.table(paste(folder, '/REVIGO_cleaned/', 'REVIGO_cluster', i, '_cleaned.tsv', sep=''), header=T)
gsea_cluster['cluster'] <- i
genes_cluster <- read.table(paste(folder, '/genelist_cluster', i, '.tsv', sep=''))
gsea[[i]] <- gsea_cluster
genelist[[i]] <- genes_cluster
}
gsea <- do.call("rbind", gsea)
genelist <- do.call("rbind", genelist)
create_terms <- function(gsea){
return(data.frame(category=gsea$gsea.domain, ID=gsea$revigo.term_ID, term=gsea$revigo.description, adj_pval=gsea$gsea.p.value, genes=gsea$gsea.intersection, cluster=gsea$cluster))
}
create_genes <- function(genelist){
return(data.frame(ID=genelist$gene_short_name, logFC=genelist$avgLogFC_State2_State3))
}
#genes_c2_swapped <- data.frame(ID=genes_c2$ID, logFC=genes_c2$logFC*-1)
All terms
terms <- create_terms(gsea)
genes <- create_genes(genelist)
circ <- circle_dat(terms, genes)


Terms associated with ECM branch
circ_metabolic <- circle_dat(terms_metabolic, genes_swapped)
Error in toupper(genes$ID) : object 'genes_swapped' not found


Only upregulated terms
gsea_upregulated <- gsea[gsea$cluster %in% c(2,6,3),]
terms_upregulated <- create_terms(gsea_upregulated)
circ_upregulated <- circle_dat(terms_upregulated, genes)
GOBar(circ_upregulated)




GOBubble(subset(circ_upregulated, category=='CC'), labels=2, ID=F, colour=c('#ff8284', '#ff8284', '#ff8284'))

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